Novel streptomyces strain with potential anti-microbial activity against phytopathogenic fungi

ABSTRACT

The present invention relates to a new strain of Streptomyces sp., called CIMAP A 1  isolated from the soil of geranium ( Pelargonium graleoleus ) planted in the experimental fields of CIMAP and having the accession No. . . . and capable of inhibiting the growth of phytopathogenic fungi.

FIELD OF THE INVENTION

[0001] The present invention relates to a new strain of Streptomyces isolated from the soil of geranium (Pelargonium graveolens) at Central Institute of Medicinal and Aeromatic Plants (CIMAP), Lucknow, India—the newly isolated strain Streptomyces CIMAP-A₁ is capable of inhibiting the growth of a wide range of phytopathogenic fungi and has been found to be highly effective in protecting rose-scented geranium from anthracnose disease caused by Colletotrichum acutatum and opium poppy from damping-off caused by Pythium dissotocurn. The said novel strain of Streptomyces has been isolated from a soil at CIMAP, where field experiments in respect of the plant Pelargonium graveolens were conducted.

BACKGROUND OF THE INVENTION

[0002] Fungal phytopathogenes cause considerable damage to the medicinal and aromatic plants. These pathogens produce various kinds of diseases whose occurrence in severe form may either kill emerging seedlings or reduce plant growth and adversely effect crop yield. Various phytopathogenic fungi including Rhizoctonia, Sclerotinia, Pythium, Fusarium, Curvularia, Alternaria, Collectotrichum and Thielavia cause different types of diseases on medicinal and aromatic plants such as stem rot and twig blight (Sclerotinia sclerotiorum) on periwinkle, Egyption henbane, and ammi majus; leaf blight (Curvularia andropogonis); lethal yellowing (Pythium aphanidermatum) and collar rot (Fusarium moniliforme) on Java citronella; damping-off (Pythium dissotocum), collar rot (Rhizoctonia solani) and leaf blight (Alternaria alternata) opium poppy; stolon and root rot (Thielavia basicola) on mints and anthracnose disease Colletotrichum acutatum on geranium. (Alam et al 1983, Indian Phytopath. 367: 480-483, ibid 1992 Plant 43:10578-1061; ibid 1996 Indian Phytopath. 49:94-97; Sattar et al 1993, Indian J. Plant Pathol 10:10-11; ibid 1999, Indian J. Plant Pathol 17:74-76).

[0003] Chemical pesticides are commonly used to protect plants from the fungal infections but their intensive and indiscriminate uses pose many serious problems such as development of resistant strains of the pathogen, build up of harmful residues in the plant parts, non-target effect on beneficial microflora and environmental pollution. Thus; to avoid such problems attention has been focused to use microorganisms such as fungi, bacteria and actinomycetes as biocontrol agents to minimize infection caused by plant pathogens.

[0004] Streptomyces spp. are commonly distributed in the soil rhizosphere and phyllosphere by which they produce strong antagonistic effect on the fungal phytopathogens and protect plants from the attack of the pathogens (Broadbent et al 1971, Aust. J. Biol. Sci 24 : 925-944, Lahdenpera 1987, Acta Horticulture 216 : 85-92, El-Abyad et al 1993. Plant and Soil, 149 ; 185-195). Streptomyces griseoviridis isolated from Finnish sphagnum peat produce strong antagonistic effect on the growth of Fusarium culmorum, Pythium debaryanum and Rhizoctonia solani and its spraying reduce the damage caused by them (Tahvonen, 1985, Vaxskyddsnotiser 49 : 86-90, White et al. 1998, In Brighton Crop Protection Conference on Pests and Diseases vol 1: 221-226). A direct evidence that the antibiotic geldamycin produced by Streptomyces hygroscopius var. geldanus suppressed the growth of Rhizoctonia solani, thus controlled Rhizoctonia root rot of pea (Rothrock and Gottlieb, 1984, Can. J. Microbiol 30 : 1440-1447).

[0005] Several Streptomyces cultures have been isolated from the soil of CIMAP experimental fields at Lucknow and they have been maintained in our culture collection. One of the isolates of Streptomyces i.e. Streptomyces CIMAP-A₁ shows strong antagonistic activities against the wide range of fungal in vitro. One of the most recent and taxonomic studies of Streptomyces was carried out in the International Streptomyces Project (I.S.P) where more than 400 type strains were examined independently by Standardized procedure (Shirling E. B. and Gottlieb D. 1968, International Journal of Systematic Bacteriology, 18: 69-186, 279-31; Ibid. 1961 International Journal of Systematic Bacteriology 22 : 265-394). Streptomyces species were assigned to seven color series i.e. blue, green, gray, red, violet, white and yellow (Pridham and Tesener, 1974, Family VII Strepomyectaceae Waksman and Henriei, 1943. I. N. Bergey's Mannual of Determinative Bacteriology, 8^(th) edn., ed Buchman, R. E. & Cibbon, N. E. pp. 747-845 Baltimore; Willams & Wilkins). Subsequently, the color series were extended to accommodate additional colors. The distinctive morphology of the sporing structures have been widely used in the characterization of Streptomyces species. The spore chain morphology determined by light microscopy and spore surface ornament determined by electronic microscopy have been considered important in many classifications. (Etlinger et al 1958, Archive fur Mikrobiologie 31,326-358, Waksman S. A. 1961, The Actinomycestes Vol.2. Classification, Identification and Description of General and Species, Baltimore : Williams and Willins, Hutter, R. 1967. Systematik de Steptomyceten. Basel & New York S Karger).

[0006] Streptomyces spp. are morphologically characterized by the production of highly branched substrate mycelium (rarely bearing spores) that further form a network of white aerial hyphae bearing spores in chain at the tip of sporogenous filament (Kustner, E, 1961, International Bulletin of Bacteriological Nomenclature and Taxonomy 11, 91-98).

OBJECT OF THE INVENTION

[0007] The main object of the present invention relates to a novel strain of Streptomyces spp. (CIMAP A₁) having potential antifungal activities and capable of reducing infection by fungal pathogens.

[0008] An another object of the invention is to use the newly isolated strain of Streptomyces spp. (CIMAP A₁) for the control of different diseases like damming-off disease of opium poppy and anthracnose disease of rose scented geranium by application in a suitable medium.

SUMMARY OF THE INVENTION

[0009] The invention provides a novel Streptomyces sp. capable of inhibiting the growth of a wide range of phytopathogenic fungi. The said strain is being deposited at International Depository and bearing accession No. . . .

DETAILED DESCRIPTION OF THE INVENTION

[0010] The present invention pertains to the isolation of a number of actinomycetes from the soil and identification of a new Streptomyces strain referred to as Streptomyces CIMAP-A₁. The strain is deposited at International Depository and bearing Accession No. . . . This strain is shown to exhibit strong antagonism towards a wide range of fungal phytopathogens that cause various kinds of diseases such as damping-off, root rot, stem rot, collar rot, twig blight, lethal yellowing, leaf blight and anthracnose as shown in Table 1. As such, this Streptomyces strain is suitable as biocontrol agent that can be used to protect plants against infection by these phytopathogens. Thus, Streptomyces CIMAP-A₁ is useful in methods for reducing the susceptibility of plant to fungi infection.

[0011] Accordingly, the novel strain of Streptomyces, Streptomyces CIMAP-A₁, has been found to inhibit growth of Streptomyces sp. and Botytis cincrea by more than 90%, of Sclerotinia sclerotiorum by more than 85%, of Curvularia spp by more than 80%, of Alternaria spp by more than 65% of Corynespora cassiicola by more than 64% of Thielavia basicola by more than 54% of Rhizoctonia solani by more than 20% of Pythium spp by more than 20% and of Fusarium spp by more than 25% in vitro.

[0012] The invention further provides information on the characterization of the strain Streptomyces CIMAP-A₁ which initially produce smooth and dull white colonies on PDA which later form discrete lichnoid colonies. In the later stages of growth, it produces a weft of aerial mycelium and turn into dark brown in color and the aerial mycelium at maturity form chain of spiral spores called orthrospores. Since species delineation within the genus Streptomyces is difficult and it requires a large amount of chemotaxonomic and molecular tests, the applicants designate the strain as Streptomyces CIMAP-A₁.

[0013] Accordingly, the invention provides a biologically pure culture of Streptomyces sp., CIMAP A₁ strain bearing accession No. . . . and capable of inhibiting the growth of phytopathogenic fungi.

[0014] Another embodiment of the invention provides a new strain of Streptomyces sp., called CIMAP A₁ isolated from the soil of geranium (Pelargonium graveolens) planted in the experimental fields of CIMAP and having the accession No. . . . and capable of inhibiting the growth of phytopathogenic fungi.

[0015] Still another embodiment of the invention provides a novel strain having the following characteristics:

[0016] a) producing smooth, dull white colonies on Poison Disk Assay (PDA) which later forms discrete and lichnoid colonies,

[0017] b) in late stages of growth, the present strain produces white aerial mycelium which later turn into dark brown in color,

[0018] c) aerial mycelium at maturity form chain of spores, and

[0019] d) exhibiting unique fingerprint pattern as shown in FIG. 3.

[0020] Still another embodiment of the present invention provides a strain Streptomyces CIMAP-A₁ having highly effective growth inhibiting properties against Sclerotinia sclerotiorum by 90%, Curvularia andropogonis by 85%, Alternaria phragmospora by 66% and Colletotrichum acutatum by 60%.

[0021] Yet another embodiment of the present invention provides a culture (CIMAP-A₁) which exhibits phytopathogenic activity against the Phytopathogenic species selected from the group comprising Rhizoctonia, Sclerotinia, Pythium, Fusarium, Curvularia, Alternaria, Colletotrichum and Thielavia.

[0022] One more embodiment of the present invention provides a method for evaluating antifungal activity of CIMAP-A₁ vitro against wide range of phytopathogenic fungi of medicinal and aromatic plants.

BRIEF DESCRIPTION OF ACCOMPANYING DRAWINGS

[0023] In the accompanying drawings,

[0024]Fig. 1a. shows cultural characteristic of Streptomyces CIMAP A₁ strain. It is clear from FIG. 1. that the isolate Streptomyces CIMAP A₁ initially produce smooth and dull white colonies on PDA which later form discrete and lichnoid colonies.

[0025]Fig. 1b. shows the enlarged view (a close-up view) of colonies characteristic of Streptomyces CIMAP A₁ strain.

[0026]Fig. 2. shows electron photomicrograph of Streptomyces CIMAP-A₁ strain.

[0027]Fig. 3. shows typical RAPD profile of the Streptomyces CIMAP-A₁ strain.

[0028]Fig. 4(a) to (d). shows in vitro inhibition in plate I by the Streptomyces CIMAP-A₁ strain of phytopathogenic fungi. (a) Sclerotinia sclerotiorum, (b) Fusarium semitectum & F. moniliformei, (c) Thielavia basicola & F. semitectum (Opium poppy) and (d) Corynespora cassiicola.

[0029]Fig. 5(a) to (d). shows in vitro inhibition of the following pathogenic fungi in plate II by the Streptomyces CIMAP-A₁ strain: (a) Rhizoctonia solani (Opium poppy), (b) Colletotrichum acutatum & Fusarium moniliforme, (c) R. solani (salvia) & Pythium dissotocum and (d) Alternaria alternata.

[0030]Fig. 3. shows typical RAPD profile of the Streptomyces CIMAP-A₁ strain.

MATERIAL AND METHODS Isolation of Streptomyces sp. From Soil

[0031] Soil samples were collected randomly from the CIMAP experimental fields at Lucknow to a depth of 0-2-cm, mixed thoroughly and stored at 5° C. in polythene bag. One gram soil samples were dissolved in 10 ml sterile distilled water (SDW) and further diluted to {fraction (1/100)}, {fraction (1/200)}, {fraction (1/500)} and {fraction (1/1000)}with SDW and stirred vigorously to obtain homogenous spores suspension. An aliquot of 0.5 ml of different dilutions was inoculated and spread over Nutrient Agar/Potato-Dextrose Agar plates which were incubated at 25 ±1° C. in dark for 3-5 days. The discrete and lichnoid colonies appearing to be Streptomyces sp. were subcultured on fresh PDA plants. The cultures were later purified by single spore isolation technique and maintained onto PDA slants under mineral oil at 25° C.

BACTERIAL GROWTH MEDIA

[0032] All bacterial growth media were prepared using distilled water and sterilized by autoclaving prior to use. All bacterial samples were handled using standard aseptic laboratory techniques to maintain purity.

PDA (Potato-Dextrose-Agar)

[0033] Potato infusion (200 g/l), dextrose (20 g/l and agar 18 g/l. This medium is available commercially from Hi-Media Laboratory, Difco Co. Potato Dextrose Broth(PDB) was made in the same manner except that agar was omitted.

NA (Nutrient Agar) Medium

[0034] 3 g/l beef extract, 5 g/l peptic digest of animal tissue and 1.5 g/l agar (HI-Media Laboratory Bombay. India) in distilled water. (pH 6.8).

Delivery Medium

[0035] The delivery medium comprising Sand/Soil/Corn meal (6:3:1) was moistened with water and was sterilized by steam sterilization prior to use. Sterilization was typically performed by autoclaving twice, each time for 60 minutes.

Harvesting of Bacterial Growth

[0036] For mycelial growth of strain Streptomyces CIMAP A_(1 ,) 500 ml Potato-Dexytose Broth (PDB) 500 ml Erlenmayer flasks were inoculated with 100 ml of stock culture and incubated on shaker with a speed 200 rpm at 25° C. for three days. Mycelia were harvested by centrifugation at 500 rpm for 10 minutes. Supernatant then decanted off and the concentrated suspension of mycelia and spores was used directly to inoculate delivery medium in the ratio of 1:10, 1:20, 1:50; 1:100. Spores of strain Streptomyces CIMAP-A₁ was also produced by growing culture for 7-10 days on solid medium (for example on PDA) Mycelia and spores were harvested from culture in Petri dishes by scrapping the surface of the agar into distilled water. The suspension of spores and mycelia in water was mixed directly into the delivery medium.

Fungal Pathogens

[0037] The cultures of fungal pathogens were obtained from the infected tissues of various medicinal and aromatic plants as listed in Table-1. They were maintained onto Potato-Dextrose-Agar or Corn meal-Agar slants under mineral oil at 20° C. in the culture collection of Department of Microbiology and Plant Pathology, CIMAP, Lucknow, India . Pathogenicity of each of the cultures was established on host the under glasshouse conditions.

Characterization of the Isolate of Streptomyces

[0038] The isolates of Streptomyces were grown on PDA and their growth characteristics (both cultural and morphological) were observed as per standardized procedure described by Shirling and Gottlib 1968 International Journal of Systematic Bacteriology 18 : 69-186). The isolate Streptomyces CIMAP-A₁ initially produce smooth and dull white colonies on PDA which later form discrete and lichnoid colonies In the later stages of growth it produces a weft white of aerial mycelium and turn into dark brown in color. The aerial mycelium at maturity form chain of spores called orthrospores..

DNA Isolation and PCR Amplification Reactions

[0039] DNA was isolated from the fungus essentially according to the protocol (Khanuja et al, 1999 Plant Molecular Biology Reporter, 17 : 74). .Polymerase chain reactions (PCRs) were carried out in 25 μ volume. A reaction tube contained 25 μg of DNA, 0.2 unit of Taq DNA polymerase, 100 μM each of dNTPs, 1.5 mM MgCl₂ and 5 ρ mol of decanucleotide Primers. The amplifications were carried out using the DNA. Engine thermal cycler (MT Research, USA) following the protocol of Shasany et al. 1998, Journal of Biosciences 23 :641-646). The amplified products were loaded in 1.2% agarose gel containing 0.5 μg ml⁻¹ of ethidium bromide and photographed by Image Master VDS system. Ten random decamer primers synthesized in the laboratory were used to prepare the fingerprint pattern of the fungs. The pattern (Fig. 3) was found to be unique incomparison with other microorganisms especially Streptomyces spp.

[0040] The invention is described in detail herein below with reference to the accompanying drawings and following examples which are provided merely to illustrate the invention and should not be construed as limitations on the inventive concept.

EXAMPLES In Vitro Testing of Antagonistic Activity of Strain Streptomyces CIMAP-A₁

[0041] The antagonistic activity of strain Streptomyces CIMAP-A₁ was tested in vitro by following common dual cultures technique on PDA (Morton DT and N. H. Stroube 1955, Phytopathology 45: 419-420) where inhibition zones in between the colonies of antagonist and pathogen was measured 6 days after inoculation and percent growth inhibition was determined as shown in table 1 and FIGS. 1 and 2. The newly isolated sdtrain of Streptomyces, Streptomyces CIMAP-A₁, was able to inhibit growth of Stremphyllum sp. and botrytis cincrea by 90%, Selerotinia sclerotiorum by 85%, Curvularia spp. By 80-85%, Alternaria spp by 66-67%, Corynespora cassiicola by 64%, Ihielavia basicola by 54% Rhizoctorion solain by 20-28% Pythium spp. By 8-20% and Fusarium spp. By 20-28 in vitro (Table 1).

In Vivo Testing of the Streptomyces CIMAP A₁ On Different Known Pathogens

[0042] Opium poppy seeds were treated with the strain of Streptomyces CIMAP-A₁ of the present invention and exposed to the fungal pathogen, P. dissotocum causing pre-emergence damming-off disease and maximum emergence of seedlings were observed which also show growth characteristic similar to the untreated unexposed control plants. Seeds treated with Streptomyces CIMAP-A₁ and exposed to the inoculum of fungal pathogen also produced plants showing growth characteristics superior to the untreated, unexposed plants.

[0043] The spray of cell free culture filtrate of Streptomyces CIMAP-A₁ on the foliage of a geranium in the commercial fields significantly reduced by fungal infection caused by Colletotrichum acutatum. The strain Streptomyces CIMAP-A₁ of the present invention produce vegetative cells or spores for incorporation into a delivery medium. The composition comprising the vegetative cells and spores of Streptomyces CIMAP-A₁ and the delivery medium has a long shelf life and is suitable for delivering the antagonisdt to plants for effective control of fungal phytopathogens.

Advantages

[0044] Streptomyces CIMAP-A₁ strain is capable of inhibiting the growth of wide range of phytopathogenic fungi including Rhizoctonia, Sclerotinia, Pythium, Fusarium, Curvularia, and Alternaria which have been causing various kinds of diseases on agricultural as well as horticultural crops. A thorough perusal of review of literature reveals that no such strain of Streptomyces has been obtained. The Streptomyces CIMAP A¹ strain has moreover novelty in showing growth inhibition of dark spored pathogenic fungi which are cosmopolitan in distribution. Therefore, it can be utilized as biocontrol agent against several plant pathogenic fungi of agricultural crops. This new strain multiplies on simple delivery medium and is cost effective and can be exploited commercially. It is non hazardous and ecofriendly in nature. TABLE 1 In vitro growth inhibition of fungal phytopathogens of some important medicinal & aromatic plants by the new strain Streptomyces - CIMAP-A ₁ S. Inhibition No. Pathogens Disease Host (%) 1. Alternaria alternata Leaf blight Menthol Mint 67.00 2. A. phragmospora -do- Opium poppy 66.00 3. Botrytis cineria Twig blight Plumbago 90.00 4. Collectotrichum Anthracnose Geranium 60.00 acutatum 5. C. gloeosporioides -do- -do- 62.00 6. Coynespora cassiicola Leaf blight -do- 64.00 7. Curvularia Leaf blight Java citronella 85.00 andropogonis 8. C. trifolii -do- Lemon grass 80.00 9. Fusarium moniliforme Collor rot Java citronella 20.00 10. F. semitectum Wilt Menthol mint 12.00 11. F. oxysporum -do- -do- 28.00 12. Pythium Lethal Java citronella 08.00 aphanidermatum yellowing 13. P. dissotocum Damping off Opium poppy 20.00 14. Rhizopus stolonifer Stem rot Periwinkle 10.00 15. Rhizoctonia solani Collar rot Opium poppy 20.00 16. -do- Wilt Geranium 28.50 17. -do- Wilt Psyllium 24.00 18. -do- Wilt Artemisia 21.00 19. Stemphyllium sp. Leaf spot Menthol mint 90.00 20. Sclerotinia Stem rot Psyllium 85.00 sclerotiorum 21. Thielavia basicola Stolon rot Menthol mint 54.00 

1. A biologically pure culture of Streptomyces sp., CIMAP A₁, strain bearing accession No. . . . and capable of inhibiting the growth of phytopathogenic fungi.
 2. A new strain of Streptomyces sp., called CIMAP A₁ isolated from the soil of geranium (Pelargonium graveolens) planted in the experimental fields of CIMAP and having the accession No. . . . and capable of inhibiting the growth of phytopathogenic fungi.
 3. A novel strain as claimed in claim 2 having the following characteristics: e) producing smooth, dull white colonies on Poison Disk Assay (PDA) which later forms discrete and lichnoid colonies, f) in late stages of growth, the present strain produces white aerial mycelium which later turn into dark brown in color, g) aerial mycelium at maturity form chain of spores, and h) exhibiting unique fingerprint pattern as shown in FIG.
 3. 4. A culture as claimed in claim 1 exhibiting phytopathogenic activity against Phytopathogenic species selected from the group comprising Rhizoctonia, Sclerotinia, Pythium, Fusarium, Curvularia, Alternaria, Colletotrichum and Thielavia.
 5. A strain Streptomyces CIMAP-A₁ as claimed in claim 1 having highly effective growth inhibiting properties against Sclerotinia sclerotiorum by 90%, Curvularia andropogonis by 85%, Alternaria phragnospora by 66% and Colletotrichum acutatum by 60%.
 6. A method for evaluating antifungal activity of CIMAP-A₁ vitro against wide range of phytopathogenic fungi of medicinal and aromatic plants. 